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Detailed information for vg0225007772:

Variant ID: vg0225007772 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25007772
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGGAAGTTGCCACCGTGCAGCGCCTTGCCGCGGGAGACGTCGATGAGCGGGTTGTCGTTCACGGAGTTGATCTCACGCTCGATGGACTTGGTGGCGGC[G/A]
CGGATAACCTCAATTTGAGGGCCGAGCCACTGTGGGGATGTCCGGAGCGCGTACCGGTCTTGCTTCGGCTTCATCAGTGGGTCGAGCTCACCAAGCTTCT

Reverse complement sequence

AGAAGCTTGGTGAGCTCGACCCACTGATGAAGCCGAAGCAAGACCGGTACGCGCTCCGGACATCCCCACAGTGGCTCGGCCCTCAAATTGAGGTTATCCG[C/T]
GCCGCCACCAAGTCCATCGAGCGTGAGATCAACTCCGTGAACGACAACCCGCTCATCGACGTCTCCCGCGGCAAGGCGCTGCACGGTGGCAACTTCCAGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.90% 8.30% 0.63% 22.22% NA
All Indica  2759 49.00% 14.00% 0.80% 36.25% NA
All Japonica  1512 98.20% 0.30% 0.00% 1.52% NA
Aus  269 92.90% 0.00% 1.86% 5.20% NA
Indica I  595 27.10% 19.00% 0.50% 53.45% NA
Indica II  465 50.80% 23.20% 0.86% 25.16% NA
Indica III  913 51.30% 5.40% 1.31% 42.06% NA
Indica Intermediate  786 61.80% 14.80% 0.38% 23.03% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 0.60% 0.00% 4.56% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 82.20% 2.20% 1.11% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0225007772 G -> A LOC_Os02g41680.1 synonymous_variant ; p.Arg365Arg; LOW synonymous_codon Average:82.224; most accessible tissue: Zhenshan97 root, score: 93.988 N N N N
vg0225007772 G -> DEL LOC_Os02g41680.1 N frameshift_variant Average:82.224; most accessible tissue: Zhenshan97 root, score: 93.988 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0225007772 G A -0.01 0.0 -0.02 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225007772 NA 3.82E-07 mr1389 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0225007772 NA 3.42E-07 mr1389 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0225007772 NA 3.01E-07 mr1038_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0225007772 NA 2.83E-07 mr1038_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0225007772 NA 3.27E-07 mr1389_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0225007772 NA 7.45E-08 mr1389_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0225007772 NA 2.76E-06 mr1457_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251